#!/usr/bin/python
import os
import sys
import stat
import massspec_toolbox_config as conf
(db_name, filename_fasta) = conf.get_dbinfo()
current_dirname = os.getcwd()
tandem_bin = conf.get_TPP_path('tandem.exe')
tandem2xml_bin = conf.get_TPP_path('Tandem2XML')
filename_fasta_pro = filename_fasta+'.pro'
filename_param_abs = '/home/taejoon/massspec-toolbox/config/tandem-isb_input_native.xml'
def tandem_taxonomy_xml(dbname=None, fasta_pro=None):
xml_list = []
xml_list.append('<?xml version="1.0"?>')
xml_list.append(' <bioml label="x! taxon-to-file matching list">')
xml_list.append(' <taxon label="%s">'%(dbname))
xml_list.append(' <file format="peptide" URL="%s" />'%(fasta_pro))
xml_list.append(' </taxon>')
xml_list.append('</bioml>')
return '\n'.join(xml_list)
def tandem_config_xml(param=None, mzxml=None, output=None, log='', seq='', taxonomy=None, dbname=None):
xml_list = []
xml_list.append('<?xml version="1.0" encoding="UTF-8"?>\n<bioml>')
xml_list.append('<note type="input" label="list path, default parameters">%s</note>'%param)
xml_list.append('<note type="input" label="spectrum, path">%s</note>'%mzxml)
#!/usr/bin/python
import os
import sys
import massspec_toolbox_config as conf
(db_name, filename_fasta) = conf.get_dbinfo()
sys.stderr.write("Use %s as DB file\n" % filename_fasta)
for filename_pepxml in os.listdir('sequest.pepxml/'):
if (not filename_pepxml.endswith('.pepxml')):
continue
filename_pepxml = os.path.join('sequest.pepxml', filename_pepxml)
filename_pepxml_tmp = filename_pepxml + '.tmp'
f_tmp = open(filename_pepxml_tmp, 'w')
f_pepxml = open(filename_pepxml, 'r')
for line in f_pepxml:
line = line.strip()
if (line.startswith('<search_database local_path="')):
f_tmp.write('<search_database local_path="%s" type="AA"/>\n' %
filename_fasta)
elif (line.startswith(
'<parameter name="list path, sequence source #1" value"')):
f_tmp.write(
'<parameter name="list path, sequence source #1" value="%s"/>\n'
% filename_fasta)
elif (line.startswith('<parameter name="first_database_name" value"')):
f_tmp.write(
'<parameter name="first_database_name" value="%s"/>\n' %
filename_fasta)
else:
f_tmp.write('%s\n' % line)